actually I used very routine way. Firstly I've  extract conformers of protein-ligand complexes from the trajectory. Than I've loaded it into pymol and visualize possible interactions. Than I've selected most representative conformers and loaded it separately into pose view to obtain 2D maps. I understand that its very routine but I had not any other alternatives.

By the way during usage of the g_hbond with the below flags

g_hbond -f fitted.trr -s complex.gro -n index.ndx  -hbm ./hb/hbmap.xpm  -life ./hb/hblife.xvg

In the index file I've specified ligand and protein as two groups.  should I define second group more accurately ( e.g only possible amino acids from the ligand binding pocket) ?
I've forced with the problem of the interpretation of the hbmap. As I understood that could be used for the monitoring of the h-bond occurring and breaking between protein and ligand during MD run. How it could be visualize to observe particular amino-acids on the first (protein) group which contribute to H-bonds ?


2013/4/24 Thomas Evangelidis <>

As I understood fconv can be used for the split several mol2 (or pdb) files which was placed in 1 model to the several pdb files, doesnt it ?

fconv can do miracles :) check it out !

fconv -h

In past I forced with some problems with  g_hbond. Is there any other way to monitor h bonds along the trajectory (e.g in vmd) ?

In contrast, I encountered problems with the H-bonds VMD plugin, that's why I resorted to g_hbond. Beware that g_hbonds will count the frequencies of salt-bridges too.
PoseView is used as the separate software or web server ( I mean that I analyze polar interactions both in pymol as well as via pose view).

If you find a way to draw the most important protein-ligand interactions throughout the trajectory with PoseView, then I would be very interested to know how.


2013/4/24 Thomas Evangelidis <>

I want to examine protein-ligand interactions observed in the md trajectory using Pymol.

For such task I have 100 snapshots of the protein-ligand complex which I've loaded into the pymol. Now I want to extract from all snapshots 100 ligands as the separate 100 objects and save it in the mol2. Actually I can do such task in the simplest way extracting all ligands in one object but I need as a result 100 mol2 files. Could someone show me example of some script which could do such tasks?

Save all ligands in a multi-mol mol2 file and then split if with fconv -s.

Also I'll be very thankful if someone can provide me with some tool which can be used for investigation of the ligand dynamics along MD trajectory ( in particular I want to visualize all binding poses and define all polar contacts along trajectory). For such task I've being used pymol as well as pose view loading snapshots to that programs but that way is not appropriate for analyzing of the ensembles of the binding poses obtained from md run.

I usually monitor H-bonds with g_hbond from GROMACS Tools and Salt-Bridges with the respective VMD plugin. Then I make a table with frequences of each polar interaction, pick up a frame that contains as many important interactions as possible, load it in PyMOL and draw dotted lines between the interacting atoms.
PS: I didn't know about PoseView plugin, it seems to be a very useful addition to PyMOL :)




Thomas Evangelidis

PhD student

University of Athens
Faculty of Pharmacy
Department of Pharmaceutical Chemistry
157 71 Athens



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